Seed caching by scatter-hoarding rodents is an important dispersal mechanism for many plant species, and the microhabitat of the caching site influences the quality and effectiveness of this dispersal. Shrub vegetation is a major determinant of microhabitat heterogeneity in the forest understory and influences both rodent activity and foraging behavior, and seed germination and seedling establishment. However, very few studies have investigated how shrubs affect this important mutualistic plant-animal interaction and how this is influenced by seed traits. In this study, we monitored rodent choices of caching microhabitat for 3564 artificial seeds that varied in size, nutrient content, and tannin content. By analyzing 1333 primary caches and 209 secondary caches, we showed that rodents selected different caching micro-habitats for seeds with different traits. Larger and more nutritious seeds were cached in shrubs more frequently than in the open, while tannin content had no effects on the probability of seeds being cached in shrubs. Furthermore, shrub cover significantly increased the distance which seeds were transported by rodents. If these caching differences apply to natural seeds and persist through seedling establishment and subsequent growth, they could play an important role in the spatial pattern of forest regeneration.